External Email - Use Caution        

Hi Woo-Suk, 

I was able to make the change however, I am still receiving the same error.  

mri_convert -at /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz

mri_convert -at /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz 

reading from /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz...

error: niiRead(): error opening file /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz

Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version 22.6.0: Fri Sep 15 13:39:52 PDT 2023; root:xnu-8796.141.3.700.8~1/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Oct 30 12:24:56 PDT 2023

Do you have any further suggestions to fix this issue? 

Thank you, 

Lauren Stephens

Lauren Stephens, MS 

Assistant Clinical Research Coordinator 

Department of Psychiatry and Behavioral Science 

Stanford University School of Medicine  

E: laurenss@stanford.edu 

P: (650)-725-1716

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Woo-Suk Tae <woostae@gmail.com>
Sent: Saturday, October 28, 2023 10:34 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

 

        External Email - Use Caution        

Hi, Lauren Stephens.

If you change some codes in trac-preproc ( in path/freesurfer/bin ), you can get  an aparc+aseg+thalnuc.nii.gz file without error, and make subthalamic nuclei related tracks.

 

#chage codes from 

set cmd = mri_binarize
    set cmd = ($cmd --i $fsdir/mri/$segname.mgz)
    set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
    set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz)

#to 

set cmd = mri_convert
    set cmd = ($cmd -i $fsdir/mri/$segname.mgz)
    set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
    set cmd = ($cmd -o $labdir/anatorig/${segname}+thalnuc.nii.gz)

Woo-Suk, Tae Ph.D.

Seoul, Korea

On Fri, Oct 6, 2023 at 11:42 PM Lauren Stephens <laurenss@stanford.edu> wrote:

        External Email - Use Caution        

Hi FreeSurfers, 

I am trying to troubleshoot an error during TRACULA preprocessing and the issue seems related to the creation of aparc+aseg+thalnuc.nii.gz.  The subregion segmentation prior to trac-all -prep was successful and mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz and other Thalamic Nuclei files were generated.  In the archives I saw two others have experienced a similar issue without a resolution in the thread.  

I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6.  I have attached the log file, log error, and my configuration file.  

Any help would be greatly appreciated!  

Thank you, 

Lauren Stephens

Lauren Stephens, MS 

Assistant Clinical Research Coordinator 

Department of Psychiatry and Behavioral Science 

Stanford University School of Medicine  

E: laurenss@stanford.edu 

P: (650)-725-1716

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

---------------------------------------------------------------------------------------- Woo-Suk, Tae  Ph.D.  Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: wstae@korea.ac.kr, woosuk.tae@gmail.com,            woostae@gmail.com ----------------------------------------------------------------------------------------

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer